[Gmod-help] Is there an interest in adding DAWGPAWS plant genome annotation pipeline to GMOD?

[James Estill]

Hello Scott and GMOD helpdesk --

I wanted to see if there would be an interest in the GMOD community for
adding the DAWGPAWS plant genome annotation pipeline as a component of
GMOD.

DAWGPAWS is a perl based annotation pipeline that seeks to facilitate
annotation of genes and transposable elements in plant genomes. It thus
includes gene annotation programs that are not part of some of the animal
centric annotation pipelines, and has a larger focus on transposable element
annotation. We used DAWGPAWS to annotate transposable elements in the maize
genome, the genes and TEs in the wheat genome, and I'm now using the
pipeline for annotation of genes and transposable elements in the Amborella
genome. DAWGPAWS has been used by other labs to annotate multiple grass
genomes, as well as cotton, strawberry, banana, sunflower, and the cucumber
genome.

The manuscript describing DAWGPAWS is at:
http://www.plantmethods.com/content/5/1/8
I am also writing a book chapter for annotation of retrotransposons in
plants that will rely heavily on the use of DAWGPAWS tools.

Primary features of DAWGPAWS:
 * facilitates splitting contigs for batch based annotation in a queue based
cluster computing environment (ie. Platform LSF )
 * incorporates ab initio and similarity search programs for gene
annotation
 * incorporates ab initio and similarity search programs for transposable
element annotation as well as support for mathematically defined repeats
 * provides tools for conversion of output from various programs into
GFF2/GFF3 format output
   - these generally all accept input from STDIN and write to STDOUT to
facilitate use in other pipelines outside of DAWGPAWS
 * provides tools for running annotation for sets of contigs in batch mode
and converting output to GFF2/GFF3 format

The project page is at:
http://dawgpaws.sourceforge.net/

The repository is at:
http://dawgpaws.svn.sourceforge.net/viewvc/dawgpaws/

A basic manual is at:
http://dawgpaws.sourceforge.net/man.html

I could write up a larger overview if you are interested, but thought I
would first send a short email to see if there was any general interest in
contributing DAWGPAWS into GMOD. DAWGPAWS is still in active development as
part of my funded research related to annotation of the Amborella genome. I
am currently adding code for gene model combiners such as EVM and developing
a similar combiner for retrotransposons.

I am also generally interested in contributing additional support for
transposable element annotation to the GMOD toolbox. I've developed some
GBROWSE glyphs that I personally find helpful for display of transposable
elements, and I would liked to see the future development of WebApollo
incorporate visualization and annotation curation tools for transposable
element annotation.

-- Jamie
-----------------------------------------
James C. Estill
JamesEstill at gmail.com
http://jestill.myweb.uga.edu
-----------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20110711/ce1d0bbd/attachment.html>